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A Commentary on Diversity Measures UniFrac in Very Small Sample Size
In phylogenetic, the diversity measures as UniFrac, weighted UniFrac, and normalized weighted UniFrac are used to estimate the closeness between two samples of genetic material sequences. These measures are widely used in microbiology to compare microbial communities. Furthermore, when the sample si...
Autores principales: | , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
SAGE Publications
2019
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6482663/ https://www.ncbi.nlm.nih.gov/pubmed/31040637 http://dx.doi.org/10.1177/1176934319843515 |
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author | Roldán Ahumada, Judith Agueda Avendaño Garrido, Martha Lorena |
author_facet | Roldán Ahumada, Judith Agueda Avendaño Garrido, Martha Lorena |
author_sort | Roldán Ahumada, Judith Agueda |
collection | PubMed |
description | In phylogenetic, the diversity measures as UniFrac, weighted UniFrac, and normalized weighted UniFrac are used to estimate the closeness between two samples of genetic material sequences. These measures are widely used in microbiology to compare microbial communities. Furthermore, when the sample size is large enough, very good results have been obtained experimentally. However, some authors do not suggest using them when the sample size is very small. Recently, it has been mentioned that the weighted UniFrac measure can be seen as the Kantorovich-Rubinstein metric between the corresponding empirical distributions of samples of genetic material. Also, it is well known that the Kantorovich-Rubinstein metric complies the metric definition. However, one of the main reasons to establish it is that the sample size is large enough. The goal of this article is to prove that the diversity measures UniFrac are not metrics when the sample size is very small, which justifies why it must not be used in that case, but yes the Kantorovich-Rubinstein metric. |
format | Online Article Text |
id | pubmed-6482663 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | SAGE Publications |
record_format | MEDLINE/PubMed |
spelling | pubmed-64826632019-04-30 A Commentary on Diversity Measures UniFrac in Very Small Sample Size Roldán Ahumada, Judith Agueda Avendaño Garrido, Martha Lorena Evol Bioinform Online Commentary In phylogenetic, the diversity measures as UniFrac, weighted UniFrac, and normalized weighted UniFrac are used to estimate the closeness between two samples of genetic material sequences. These measures are widely used in microbiology to compare microbial communities. Furthermore, when the sample size is large enough, very good results have been obtained experimentally. However, some authors do not suggest using them when the sample size is very small. Recently, it has been mentioned that the weighted UniFrac measure can be seen as the Kantorovich-Rubinstein metric between the corresponding empirical distributions of samples of genetic material. Also, it is well known that the Kantorovich-Rubinstein metric complies the metric definition. However, one of the main reasons to establish it is that the sample size is large enough. The goal of this article is to prove that the diversity measures UniFrac are not metrics when the sample size is very small, which justifies why it must not be used in that case, but yes the Kantorovich-Rubinstein metric. SAGE Publications 2019-04-23 /pmc/articles/PMC6482663/ /pubmed/31040637 http://dx.doi.org/10.1177/1176934319843515 Text en © The Author(s) 2019 http://www.creativecommons.org/licenses/by-nc/4.0/ This article is distributed under the terms of the Creative Commons Attribution-NonCommercial 4.0 License (http://www.creativecommons.org/licenses/by-nc/4.0/) which permits non-commercial use, reproduction and distribution of the work without further permission provided the original work is attributed as specified on the SAGE and Open Access pages (https://us.sagepub.com/en-us/nam/open-access-at-sage). |
spellingShingle | Commentary Roldán Ahumada, Judith Agueda Avendaño Garrido, Martha Lorena A Commentary on Diversity Measures UniFrac in Very Small Sample Size |
title | A Commentary on Diversity Measures UniFrac in Very Small Sample Size |
title_full | A Commentary on Diversity Measures UniFrac in Very Small Sample Size |
title_fullStr | A Commentary on Diversity Measures UniFrac in Very Small Sample Size |
title_full_unstemmed | A Commentary on Diversity Measures UniFrac in Very Small Sample Size |
title_short | A Commentary on Diversity Measures UniFrac in Very Small Sample Size |
title_sort | commentary on diversity measures unifrac in very small sample size |
topic | Commentary |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6482663/ https://www.ncbi.nlm.nih.gov/pubmed/31040637 http://dx.doi.org/10.1177/1176934319843515 |
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